sp. nov., isolated from anoxic soil under the treatment of reductive soil disinfestation.

Reductive soil disinfestation (RSD), also known as biological soil disinfestation, is a bioremediation method used to suppress soil-borne plant pathogens by stimulating the activity of indigenous anaerobic bacteria in the soil. An anaerobic bacterial strain (E14) was isolated from an anoxic soil sample subjected to RSD treatment and then comprehensively characterized. Cells of the strain were Gram-stain-positive, curved to sigmoid, and spore-forming rods.

sp. nov., a facultatively anaerobic, propionate-producing bacterium isolated from a methanogenic reactor treating waste from cattle farms.

Facultatively anaerobic bacterial strains were isolated from samples of a methanogenic reactor and, based on 16S rRNA gene sequences, found to be affiliated with the family in the phylum Four strains with almost-identical 16S rRNA gene sequences were comprehensively characterized. The most closely related species to the strains was BL-34 (96.4 % sequence similarity).

Copper ion (Cu2+) is involved in the transcription of the tyrosinase-encoding melB gene of Aspergillus oryzae in solid-state culture.

In Aspergillus oryzae, the tyrosinase-encoding gene melB causes undesirable browning of sake and sake lees. This gene is known to be expressed specifically in solid-state culture; however, its expression mechanisms remain unknown. Here, we evaluated the possible factors affecting the transcription of melB and found that the copper ion (Cu2+) significantly enhanced the transcription level of melB in solid-state culture.

sp. nov., a plant polysaccharide-decomposing anaerobic bacterium isolated from a methanogenic reactor.

An obligately anaerobic bacterial strain (WR041) was isolated from a plant residue sample in a methanogenic reactor. Cells of the strain were Gram-stain-negative, non-motile, non-spore-forming rods. JCM 13650 was the closest species of the strain based on 16S rRNA gene sequencing (98.

sp. nov., a chitin-decomposing anaerobic bacterium isolated from anoxic soil subjected to biological soil disinfestation.

An obligately anaerobic bacterial strain (CTTW) belonging to the family within the class was isolated from an anoxic soil sample subjected to biological or reductive soil disinfestation. Cells of the strain were Gram-stain-positive, short rods with peritrichous flagella. The strain was saccharolytic and decomposed polysaccharides, chitin, xylan and β-1,3-glucan.

Cyclohumulanoid Sesquiterpenes from the Culture Broth of the Basidiomycetous Fungus .

A series of cyclohumulanoids, i.e., tricocerapicanols A-C (-), tricoprotoilludenes A () and B (), tricosterpurol (), and tricoilludins A-C (-) were isolated along with known violascensol () and omphadiol () from the culture broth of , an inedible but not toxic mushroom.

sp. nov., a new β-1,3-glucan-decomposing bacterium isolated from anoxic soil subjected to biological soil disinfestation.

Biological soil disinfestation (BSD) or reductive soil disinfestation (RSD) is a bioremediation method used to suppress or eliminate soil-borne plant pathogens by stimulating activities of indigenous anaerobic bacteria of the soil. An anaerobic bacterial strain (TW1) was isolated from an anoxic soil sample subjected to the BSD treatment and comprehensively characterized. Cells of the strain were Gram-stain-positive, slightly curved and motile rods producing terminal spores.

Identification of neomacrophorins isolated from Trichoderma sp. 1212-03 as proteasome inhibitors.

Neomacrophorins I-III (1-3) and X have previously been isolated from Trichoderma sp. 1212-03. Their mode of action against cancer cells and the mechanism of biosynthesis of the characteristic [4.

DFT calculation-assisted stereo-structural assignment of arundifungin.

Arundifungin (1) has been reported as a potent antifungal agent against Candida and Aspergillus spp; however, only its planar structure has been disclosed. This paper describes the assignment of the relative and absolute configuration of 1, which includes (a) determination of the relative configuration of the ABCD polycyclic ring moiety on the basis of detailed nuclear magnetic resonance (NMR) analysis, followed by the confirmation with density functional theory (DFT)-based C NMR chemical shift calculations, (b) determination of the absolute configuration of the ABCD polycyclic ring moiety by observing a positive Cotton effect at 217 nm because of the C-8/C-9 tetrasubstituted double bond and its reproduction using DFT calculations, (c) determination of the configurational relationship between C-17 and C-20 by a combination of nuclear Overhauser effect (NOE) analysis and DFT-based conformational analysis, and (d) determination of the relative and absolute configuration of the C-24 and C-25 asymmetric centers on the acyclic side chain by a combination of chemical derivatization including modified Mosher's method and DFT-based conformational analysis, followed by electronic circular dichroism (ECD) spectral reproduction. Present study also discovered 26-deoxyarundifungin (2) of which relative structure was readily elucidated by H and C spectral comparison with those of 1.

Capsulimonas corticalis gen. nov., sp. nov., an aerobic capsulated bacterium, of a novel bacterial order, Capsulimonadales ord. nov., of the class Armatimonadia of the phylum Armatimonadetes.

An aerobic bacterial strain designated AX-7 was isolated from the trunk surface of a Japanese beech (Fagus crenata). Cells of strain AX-7 were Gram-stain-negative, non-spore-forming, non-motile rods (1.0-1.

Description of Deinococcus populi sp. nov. from the trunk surface of a Japanese aspen tree.

A bacterial strain designated PtRA-8 was isolated from the trunk surface of a Japanese aspen tree (Populus tremula var. sieboldii). Cells of strain PtRA-8 were aerobic, non-motile, non-spore forming, Gram-stain-negative rods, 1.

Neomacrophorin X, a [4.4.3]Propellane-Type Meroterpenoid from Trichoderma sp. 1212-03.

Neomacrophorin X (1) was isolated from Trichoderma sp. 1212-03. Heteronuclear multiple bond correlation (HMBC) spectral analysis indicated a unique [4.

Acidicapsa acidisoli sp. nov., from the acidic soil of a deciduous forest.

A bacterial strain designated strain SK-11 was isolated from the acidic soil of a deciduous forest in the Shirakami Mountains in Japan. Cells of strain SK-11 were aerobic, non-motile, Gram-stain-negative rods, 0.7-1.

Draft Genome Sequence of Bacteroidales Strain 6E, Isolated from a Rice Paddy Field in Japan.

We generated a high-quality draft genome sequence of Bacteroidales strain 6E, a strict anaerobe newly isolated from Japanese rice paddy field soil. The genome consists of 61 contigs, with a total size of 4,436,542 bp and mean G+C content of 45.4%.

Relative and absolute structure of phomolide C.

Phomolide C (1) was isolated from a fungus Diaporthe sp. being found at Shirakami mountainous area. Although only the planar structure of 1 has been known, our detailed NMR spectroscopic analysis and ECD studies revealed its both relative and absolute configuration.

Clostridium oryzae sp. nov., from soil of a Japanese rice field.

An obligately anaerobic bacterial strain designated KC3(T) was isolated from a rice straw-degrading culture, for which soil of a Japanese rice field was used as the inoculum. Cells of strain KC3(T) were determined to be non-cellulolytic, Gram-stain-positive, non-motile, ellipsoidal, spore-forming rods, 0.8-1×4-25 µm.

Genetic polymorphisms in Japanese fragrant landraces and novel fragrant allele domesticated in northern Japan.

Rice fragrance is an important characteristic for Southeast Asian consumers, and fragrant landraces from Japan were first recorded in the 17th century. Principal component analysis clearly showed that Japanese fragrant landraces were genetically different from non-Japanese fragrant landraces. Japanese fragrant landraces were composed of six clades, none of which carried the most common fragrance mutation, an 8-bp deletion in exon 7 of Badh2.

Roseomonas aceris sp. nov. isolated from a mono maple tree in the Shirakami Mountains in Japan.

A novel bacterial strain belonging to the genus Roseomonas was isolated from the trunk surface of a mono maple (Acer mono) tree growing in the Shirakami Mountains. The strain, designated R-1(T), was Gram-negative, non-motile, and oval-rod, and formed reddish colonies on agar plates, as has previously been described for Roseomonas species. Although motility was not observed, cells were peritrichously flagellated.

Paenibacillus shirakamiensis sp. nov., isolated from the trunk surface of a Japanese oak (Quercus crispula).

A novel bacterial strain designated P-1T was isolated from the trunk surface of a Japanese oak (Quercus crispula) growing in the Shirakami Mountains in Japan. Cells of strain P-1T were Gram-stain-negative, ellipsoidal endospore-forming, aerobic, slightly acidophilic rods, 0.8×2-5 µm, and motile by means of peritrichous flagella.

Description of Anaerobacterium chartisolvens gen. nov., sp. nov., an obligately anaerobic bacterium from Clostridium rRNA cluster III isolated from soil of a Japanese rice field, and reclassification of Bacteroides cellulosolvens Murray et al. 1984 as Pseudobacteroides cellulosolvens gen. nov., comb. nov.

An obligately anaerobic bacterial strain designated T-1-35(T) was isolated as a dominant cultivable cellulose-degrading bacterium from soil of a Japanese rice field as an anaerobic filter-paper degrader. Cells of strain T-1-35(T) stained Gram-positive and were non-spore-forming rods with rounded ends, 0.8-1.

Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field.

A novel anaerobic bacterium that could ferment amino acids and organic acids was isolated from an anaerobic, propionate-oxidizing enrichment culture originating from soil of a rice field in Japan. Cells of the isolate, designated strain 4F6E(T), were Gram-staining-negative, oxidase- and catalase-negative, non-spore-forming, vibrio-shaped, motile rods (0.8×2.

Brevibacterium yomogidense sp. nov., isolated from a soil conditioner made from poultry manure.

A novel Gram-stain-positive rod-shaped actinobacterium was isolated from a soil conditioner made from poultry manure. The isolate, designated strain MN-6-a(T), contained anteiso-C(15 : 0) and anteiso-C(17 : 0) as the major fatty acids, and MK-7(H(2)) and MK-8(H(2)) as the major menaquinones. Phosphatidylglycerol was a major polar lipid.